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Thursday, December 30, 2010

The 100th Blue Obelisk 2006 paper citation

Two and a half months after the CDK milestone, the Blue Obelisk paper also reached 100 citations. Here the lucky paper is Design, Synthesis, and Preclinical Evaluation of New 5,6- (or 6,7-) Disubstituted-2-(fluorophenyl)quinolin-4-one Derivatives as Potent Antitumor Agents by Chou et al (doi:10.1021/jm100780c). The Blue Obelisk paper (doi:10.1021/ci050400b) is cited because the authors used OpenBabel. About half of the 100 citations is because OpenBabel was used, whereas OpenBabel is only mentioned as one of the Blue Obelisk-associated unprojects in the Blue Obelisk paper.

I am not sure how this habit started, but with citation practices, it is unlikely to go away. But who am I to complain....

// Second program DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR); engine.process(molecule);

/** * The function getProperties returns a Map value. Map represents a Key Value set. * It is retrieved using an iterator. Since the key is of DescriptorSpecification class and the * value is of type DescriptorValue we have to typecast the key and value with the same while retrieving. * since they have not override the same to String. */ Map i = molecule.getProperties(); Iterator iterator = i.keySet().iterator();

the output is different for windows and linux. while i get only a bcut descriptor o/p for standalone and netbeans 6.8 in linux, around 40 descriptors are given as o/p in windows using netbeans 6.8... please advice

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This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!

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